Hi Carlos,
No, the mdcrd file is fill at least It have coordinates...Ok I'll
start again and check the structure.
Thanks so much
Myriam
Carlos Simmerling <carlos.simmerling.gmail.com> escribió:
> minimization can't always correct very bad initial structures. you should
> look at the structure and try to determine the problem. It may be that you
> need to make some adjustments (using a program like Chimera) before
> minimization. This is really an issue with how you generated the initial
> structure.
>
> for the checkstructure error, are you sure the mdcrd file is not empty?
>
> On Tue, Jan 12, 2021 at 12:20 PM MYRIAN TORRES RICO <
> myriam.torres.iiq.csic.es> wrote:
>
>> Ok, I have launched checkstructure in the min step and indeed I get a
>> couple of residues very close to each other, my problem is that even
>> minimizing it, this problem is not corrected...
>>
>> Another question, when I use checkstructure in the pressure step, it
>> does not recognize my file.mdcrd and I get the following error
>>
>> Reading 'smp-193-ptn3rig.top' as Amber Topology
>> Radius Set: H (N) -modified Bondi radii (mbondi2)
>> INPUT: Reading input from 'coordprobe.in'
>> [parm smp-193-ptn3rig.top]
>> Warning: Topology 'smp-193-ptn3rig.top' already present.
>> Warning: To load the same topology file multiple times use tags,
>> Warning: e.g. `parm <file> [tag]`.
>> [trajin smp-193ptn_pcon_tar.mdcrd]
>> Reading 'smp-193ptn_pcon_tar.mdcrd' as Amber NetCDF
>> Error: Netcdf file is empty.
>> Error: Could not set up 'smp-193ptn_pcon_tar.mdcrd' for reading.
>> Error: Could not set up input trajectory 'smp-193ptn_pcon_tar.mdcrd'.
>> 1 errors encountered reading input.
>> TIME: Total execution time: 0.1422 seconds.
>> Error: Error (s) occurred during execution.
>>
>> I need to change the format, right?
>>
>>
>> Thanks in advance,
>>
>> Myriam
>>
>>
>>
>> Carlos Simmerling <carlos.simmerling.gmail.com> escribió:
>>
>> > go all the way back to the first step after building the structure, and
>> the
>> > first energy output in that file. what does it say? is it a minimization
>> > step?
>> > you can use cpptraj to check for close contacts in your input
>> coordinates,
>> > this was discussed very recently here and you can find the emails in the
>> > archive on ambermd.org
>> > this post may be useful as well
>> > http://archive.ambermd.org/201906/0336.html
>> >
>> > On Tue, Jan 12, 2021 at 10:11 AM MYRIAN TORRES RICO <
>> > myriam.torres.iiq.csic.es> wrote:
>> >
>> >> Ok, I have checked the previous steps (minimization and heating) and
>> >> in both, all the bond energies fluctuate a lot and indeed that of VDW
>> >> is so high that it appears with (*).
>> >> Knowing this ... how do I fix it? because the input comes from a
>> >> previous docking and in the LEAP it didn't give me any problems...
>> >>
>> >> Thanks so much in advance,
>> >>
>> >>
>> >> Myriam
>> >>
>> >>
>> >> Carlos Simmerling <carlos.simmerling.gmail.com> escribió:
>> >>
>> >> > your initial structure looks to have extremely high VDW energies. You
>> >> > should check the end of the heating step that generated the
>> coordinates
>> >> > used as input here, and see if the energy was ok or not. If it was ok
>> >> there
>> >> > but not here, something must be different about the 2 runs.
>> >> >
>> >> > On Tue, Jan 12, 2021 at 9:38 AM MYRIAN TORRES RICO <
>> >> > myriam.torres.iiq.csic.es> wrote:
>> >> >
>> >> >> Hi,
>> >> >>
>> >> >> I have launched again my script with nstlim=10 and ntpr=1 but I
>> >> >> haven't find differences...(I have attached the new output).
>> >> >>
>> >> >> Thanks in advance
>> >> >>
>> >> >>
>> >> >> myriam
>> >> >> David A Case <david.case.rutgers.edu> escribió:
>> >> >>
>> >> >> > On Tue, Jan 12, 2021, MYRIAN TORRES RICO wrote:
>> >> >> >>
>> >> >> >> I have attached the output file where the error appears, in case
>> it
>> >> >> >> was helpful. If you need others files, tell me.
>> >> >> >
>> >> >> > Try setting nstlim=10 and ntpr=1. That might give you some
>> >> information.
>> >> >> >
>> >> >> > ....dac
>> >> >> >
>> >> >> >
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Received on Thu Jan 14 2021 - 01:00:02 PST
